// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
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  //
  // ******************************************************************************
  package ffx.algorithms.commands;
  
  import static org.junit.Assert.assertEquals;
  
  import ffx.algorithms.misc.AlgorithmsTest;
  import ffx.algorithms.optimize.anneal.SimulatedAnnealing;
  import java.util.Arrays;
  import java.util.Collection;
  import org.junit.Test;
  import org.junit.runner.RunWith;
  import org.junit.runners.Parameterized;
  import org.junit.runners.Parameterized.Parameters;
  
  /** @author Hernan Bernabe */
  @RunWith(Parameterized.class)
  public class AnnealTest extends AlgorithmsTest {
  
    private static final double tolerance = 0.01;
    private String info;
    private String filename;
    private double endKineticEnergy;
    private double endPotentialEnergy;
    private double endTotalEnergy;
    private double endTemperature;
  
    public AnnealTest(String info, String filename, double endKineticEnergy,
                      double endPotentialEnergy, double endTotalEnergy, double endTemperature) {
      this.info = info;
      this.filename = filename;
      this.endKineticEnergy = endKineticEnergy;
      this.endPotentialEnergy = endPotentialEnergy;
      this.endTotalEnergy = endTotalEnergy;
      this.endTemperature = endTemperature;
    }
  
    @Parameters
    public static Collection<Object[]> data() {
      return Arrays.asList(
          new Object[][] {{"Acetamide with Stochastic integrator for Simulated Annealing Test", // info
              "acetamide_annealing.xyz", // filename
              2.7348819613719866, // endKineticEnergy
              -30.162204159002336, // endPotentialEnergy
              -27.427322197628616, // endTotalEnergy
              101.94414998339263 // endTemperature
          }});
    }
  
    @Test
    public void testSimulatedAnnealing() {
  
      // Set-up the input arguments for the script.
      String[] args = {"-n", "200", "-i", "STOCHASTIC", "-r", "0.001", "--tl", "100", "--tu", "400",
          "--tmS", "EXP", "-W", "10", "-w", "100", "-k", "100", getResourcePath(filename)};
      binding.setVariable("args", args);
      binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
  
      Anneal anneal = new Anneal(binding).run();
      algorithmsScript = anneal;
  
      SimulatedAnnealing simulatedAnnealing = anneal.getAnnealing();
  
      // Assert that end energies are within the tolerance for the dynamics trajectory
     assertEquals(info + " Final kinetic energy", endKineticEnergy, simulatedAnnealing.getKineticEnergy(), tolerance);
     assertEquals(info + " Final potential energy", endPotentialEnergy, simulatedAnnealing.getPotentialEnergy(), tolerance);
     assertEquals(info + " Final total energy", endTotalEnergy, simulatedAnnealing.getTotalEnergy(), tolerance);
     assertEquals(info + " Final temperature", endTemperature, simulatedAnnealing.getTemperature(), tolerance);
   }
 }